Night-time won't make the process any more, or less, risky. It's pretty straightforward, and following the guidance in this thread and elsewhere on FT should ease you through it.

Still, back-to-back connection isn't a standard international transfer, so you might be quizzed if the immigration officer is new to QR shenanigans or wants to be awkward.

You won't get a boarding card anywhere but Cairo. Your itinerary print out or QR's acknowledgment of your on-line check-in will be sufficient, subject to the caveat outlined above.

With the cost if a visa and a night in an airport hotel less than $100, I'd take the easier, hassle-free route.